RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Yu9FGf/RM_319099.ThuApr171001412025 Search Engine = rmblast 2.13.0+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.4 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1744909300 Database = /dev/shm/rModeler.Yu9FGf/GCA_965119315.1_aPelLes1.hap2.1 - Sequences = 977 - Bases = 5762139629 - N50 = 672873637 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 832726610-892207011 | [ 1 ] 773246209-832726609 | [ ] 713765808-773246208 | [ 1 ] 654285408-713765808 | [ 2 ] 594805007-654285407 | [ ] 535324606-594805006 | [ 1 ] 475844205-535324605 | [ ] 416363805-475844205 | [ ] 356883404-416363804 | [ ] 297403003-356883403 | [ 2 ] 237922602-297403002 | [ 2 ] 178442202-237922602 | [ 4 ] 118961801-178442201 | [ ] 59481400-118961800 | [ ] 1000-59481400 |************************************************** [ 964 ] Storage Throughput = excellent ( 1805.75 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40021242 bp ( 40019042 non ambiguous ) - Num Contigs Represented = 61 - Sequence extraction : 00:05:22 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:38 (hh:mm:ss) Elapsed Time Round Time: 00:18:54 (hh:mm:ss) Elapsed Time : 979 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18234 repeats masked totaling 4971007 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10030583 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10029583 bp After Masking: 4119561 bp Masked: 58.93 % -- Input Database Coverage: 10030583 bp out of 5762139629 bp ( 0.17 % ) Sampling Time: 00:02:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:06 (hh:mm:ss) Elapsed Time, 15100 HSPs Collected Number of families returned by RECON: 1577 Round Time: 00:05:30 (hh:mm:ss) Elapsed Time : 22 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:04:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 53981 repeats masked totaling 15242551 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30030579 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 30029379 bp After Masking: 11716511 bp Masked: 60.98 % -- Input Database Coverage: 40061162 bp out of 5762139629 bp ( 0.70 % ) Sampling Time: 00:06:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:11:29 (hh:mm:ss) Elapsed Time, 71955 HSPs Collected Number of families returned by RECON: 4958 Round Time: 00:19:00 (hh:mm:ss) Elapsed Time : 134 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:12:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 171442 repeats masked totaling 47109100 bp(s). - TE Masking time 00:01:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90026575 bp Num Contigs Represented = 90 Non ambiguous bp: Initial: 90016375 bp After Masking: 33514575 bp Masked: 62.77 % -- Input Database Coverage: 130087737 bp out of 5762139629 bp ( 2.26 % ) Sampling Time: 00:20:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 00:55:41 (hh:mm:ss) Elapsed Time, 366407 HSPs Collected Number of families returned by RECON: 13299 Round Time: 01:20:54 (hh:mm:ss) Elapsed Time : 621 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:36:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 593393 repeats masked totaling 160656200 bp(s). - TE Masking time 00:05:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270052215 bp Num Contigs Represented = 185 Non ambiguous bp: Initial: 270027676 bp After Masking: 82070739 bp Masked: 69.61 % -- Input Database Coverage: 400139952 bp out of 5762139629 bp ( 6.94 % ) Sampling Time: 00:59:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22919835 Comparison Time: 05:05:34 (hh:mm:ss) Elapsed Time, 962690 HSPs Collected Number of families returned by RECON: 31831 Round Time: 06:28:59 (hh:mm:ss) Elapsed Time : 1597 families discovered. RepeatScout/RECON discovery complete: 3353 families found Classification Time: 01:02:35 (hh:mm:ss) Elapsed Time Program Time: 09:35:52 (hh:mm:ss) Elapsed Time